Is CDAN1 p.Pro159= (c.477C>T) pathogenic?

CDAN1 p.Pro159= (c.477C>T) is classified Benign/Likely benign in CDAN1 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-02-03). Common (popmax 39.5%, afr) — too common for a highly-penetrant pathogenic allele; Associated with anemia, congenital dyserythropoietic, type 1a.

What condition is associated with CDAN1 p.Pro159= (c.477C>T)?

CDAN1 p.Pro159= (c.477C>T) is associated with anemia, congenital dyserythropoietic, type 1a, congenital dyserythropoietic anemia type 1 (ClinVar).

How is Congenital dyserythropoietic anemia type I inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CDAN1 p.Pro159=

Q: How common is CDAN1 p.Pro159= (c.477C>T) in the general population?

CDAN1 p.Pro159= (c.477C>T) is common (popmax 39.5%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.477C>T · rs7167392 · VCV262378

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Common

common (popmax 39.5%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

anemia, congenital dyserythropoietic, type 1a

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.02	GERP -0.38, phastCons 0.002
Overall
CADD	9.922	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 39.5% African / African-American · 29,635/74,932 alleles

Filtering AF 39.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 39%

Overall 22.9% 368,714/1,611,732 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	39.5%	3
South Asian	36.8%	3
Ashkenazi Jewishnot grpmax-eligible	28%	4
Middle Eastern	25.8%	4
Finnishnot grpmax-eligible	25.2%	4
Remaining individualsnot grpmax-eligible	23.2%	4
European (non-Finnish)	21.5%	5
Admixed American	12.8%	8
Amishnot grpmax-eligible	9.47%	11
East Asian	8.49%	12

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDAN1
Protein: p.Pro159=
Coding: c.477C>T
MANE Select: NM_138477
dbSNP: rs7167392
Type: single nucleotide variant
Location: chr15:42736394 (GRCh38)
Gene constraint: LOEUF 0.908 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.58 · 2 PDB
Residue 159: the 'disordered' region

Full CDAN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

anemia, congenital dyserythropoietic, type 1a — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: congenital dyserythropoietic anemia type 1

For Congenital dyserythropoietic anemia type I (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

CDAN1 p.Arg1042Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Arg682Ter Pathogenic ★★ same condition
CDAN1 p.Arg714Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Asn599Ser Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Phe52Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Pro1130Leu Pathogenic/Likely pathogenic ★★ same condition
CDAN1 p.Pro51Leu Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Pro672Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdan1-p-pro159 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown